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Sample GSM3878583 Query DataSets for GSM3878583
Status Public on Jun 04, 2020
Title PD03-MK-3
Sample type SRA
 
Source name C57BL6/J WT mESC_PD03-MK
Organism Mus musculus
Characteristics strain background: C57BL6/J
cell type: Embryonic stem cell
culture condition: Akt/MAPK signal-inhibitor containing medium (PD-MK)
Growth protocol WT mESCs derived from inbred mouse (Bruce 4 C57BL/6J, male, EMD Millipore, Billerica, MA) were cultured on either LN511 coated dish under either Std (StemSure D-MEM [Wako Pure Chemicals, Osaka, Japan], 15% of fetal bovine serum, 0.1 mM β-mercaptoethanol, 1x MEM nonessential amino acids [Wako Pure Chemicals], a 2 mM L-alanyl-L-glutamine solution [Wako Pure Chemicals], 1000 U/mL LIF [Wako Pure Chemicals], 20 mg/ mL gentamicin [Wako Pure Chemicals]), 2i (Std + 1 µM PD0325901 [CS-0062, Chem Scene], 3 µM CHIR99021 [034-23103, Wako Pure Chemicals]) or PD-MK (Std medium + 1 µM PD0325901 [CS-0062, Chem Scene], 4 µM MK-2206 2HCl [S1078, Selleck Chemicals, Houston TX]) medium.
Extracted molecule total RNA
Extraction protocol RNA was extracted from either Std/LN511, 2i/LN511 or PDMK/LN511 conditioned cells at 70% confluency in a well of a 6-well plate using RNeasy Plus Mini (Qiagen).
Bulk RNA-Seq was performed by CEL-Seq2 method (Hashimshony et al., 2016) with total RNA amounts were used the range of 30-60 ng.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description PD03-MK-3_cs2_sample_0003
Data processing All reads were aligned to the reference genome (GRCm38) using HISAT (v.2.1.0)
The software HTSeq (Anders et al., 2015) was used in calculating gene-wise unique molecular identifier (UMI) counts which were converted into transcript counts after collision probability correction (Grün et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: umi_counts.txt includes read count data for each sample.
 
Submission date Jun 12, 2019
Last update date Jun 04, 2020
Contact name Itoshi NIKAIDO
E-mail(s) itoshi.nikaido@riken.jp
Organization name RIKEN
Department Center for Biosystems Dynamics Research
Lab Laboratory for Bioinformatics Research
Street address 2-1 Hirosawa
City Wako
State/province Saitama
ZIP/Postal code 351-0198
Country Japan
 
Platform ID GPL18480
Series (2)
GSE132592 RNA-seq analysis of mouse embryonic stem cells cultured in medium containing MEK and Akt inhibitors
GSE132593 Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells
Relations
BioSample SAMN12037641
SRA SRX6047937

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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